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- PDB-1wli: L122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (... -

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Basic information

Entry
Database: PDB / ID: 1wli
TitleL122Y mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
ComponentsFMN-binding protein
KeywordsELECTRON TRANSPORT / Flavoprotein / FMN
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN-binding protein
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.6 Å
AuthorsShibata, N. / Higuchi, Y.
CitationJournal: J.Biochem. / Year: 2007
Title: Determination of the role of the Carboxyl-terminal leucine-122 in FMN-binding protein by mutational and structural analysis.
Authors: Kitamura, M. / Terakawa, K. / Inoue, H. / Hayashida, T. / Suto, K. / Morimoto, Y. / Yasuoka, N. / Shibata, N. / Higuchi, Y.
History
DepositionJun 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMN-binding protein
B: FMN-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3194
Polymers26,4062
Non-polymers9132
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-21 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.673, 79.391, 39.970
Angle α, β, γ (deg.)90.00, 91.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FMN-binding protein


Mass: 13203.083 Da / Num. of mol.: 2 / Mutation: L122Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria)
Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Production host: Escherichia coli (E. coli) / References: UniProt: Q46604
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG6000, sodium acetate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU
DetectorType: OXFORD / Detector: CCD / Date: Dec 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. all: 29692 / Num. obs: 29692 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.6→1.66 Å / % possible all: 84.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: AB INITIO
Starting model: 1FLM

1flm


Resolution: 1.6→8 Å / Num. parameters: 8895 / Num. restraintsaints: 8133 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1414 5 %RANDOM
Rwork0.153 ---
all0.153 27871 --
obs0.153 27871 93.1 %-
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2177
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 62 255 2222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_zero_chiral_vol0.045
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rwork: 0.157

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